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Title: Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

Abstract

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversitymore » while still capturing rarer taxa in concert with decreasing replicate variation.« less

Authors:
 [1];  [2];  [1];  [3]
  1. Arizona State Univ., Mesa, AZ (United States)
  2. CSIRO Agriculture, Glen Osmond, SA (Australia)
  3. Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology
Publication Date:
Research Org.:
Arizona State Univ., Mesa, AZ (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1280873
Grant/Contract Number:  
SC0004601
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DNA extraction; fungal community; microbial ecology; sample size; microbial diversity; black-box; pipeline; strategy; ecology; roots

Citation Formats

Penton, C. Ryan, Gupta, Vadakattu V. S. R., Yu, Julian, and Tiedje, James M. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons. United States: N. p., 2016. Web. doi:10.3389/fmicb.2016.00824.
Penton, C. Ryan, Gupta, Vadakattu V. S. R., Yu, Julian, & Tiedje, James M. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons. United States. https://doi.org/10.3389/fmicb.2016.00824
Penton, C. Ryan, Gupta, Vadakattu V. S. R., Yu, Julian, and Tiedje, James M. Thu . "Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons". United States. https://doi.org/10.3389/fmicb.2016.00824. https://www.osti.gov/servlets/purl/1280873.
@article{osti_1280873,
title = {Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons},
author = {Penton, C. Ryan and Gupta, Vadakattu V. S. R. and Yu, Julian and Tiedje, James M.},
abstractNote = {We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.},
doi = {10.3389/fmicb.2016.00824},
url = {https://www.osti.gov/biblio/1280873}, journal = {Frontiers in Microbiology},
issn = {1664-302X},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {6}
}

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Cited by: 5 works
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Works referenced in this record:

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    Works referencing / citing this record:

    Making big data smart—how to use metagenomics to understand soil quality
    journal, March 2017


    Effect of LSU and ITS genetic markers and reference databases on analyses of fungal communities
    journal, November 2018